Schematic heat map showing the distribution of matches to the model across the genome.
The hit distribution of HERV3 across the chromosomes. More...
As many TE entries match hundreds of thousands of instances in a given genome, it is difficult to provide all matches via a web interface or as a multiple sequence alignment. In order to provide access to the matches, the graphic below has been developed that presents the distribution of hits organized on a karyotype ideogram. Hits are binned in 1 Mbp regions, with counts in each bin distinguished by colour and with bin sizes specific to each model. When a region of the hit-distribution ideogram is clicked, the hits in that region will be loaded below the karyotype ideogram. Each hit can be expanded to reveal the alignment between the hit sequence and the model. A full listing of hits (but not alignments) for an entry may be retrieved from the download page. All hits can be download as a tab delimited file from here.
By default, the page represents non-redundant hits (hits for which this model is deemed to fit the sequence better than any other Dfam model), but the image and hit lists can be toggled to show redundant hit distributions (including hits that score higher against other models). The ideogram can also be toggled to reveal the canonical Giemsa stain banding of the chromosomes, providing a reference to positional context. It is important to remember TEs split by more recently mobile TEs have not been aggregated, so older fragmented TEs may be counted as multiple instances.
There are 319 non-redundant hits in Homo sapiens.
The total number of hits is 7781.
Please click on the image above to see detailed information about a specific chromosomal region.